NAME

       NEXUSvalidator - validate NEXUS file

DESCRIPTION

       NEXUSvalidator takes reads a file and exits with a success (return code 0) if the file is valid.

   The most common usage is simply:
              NEXUSvalidator <path to NEXUS file>

OPTIONS

       -h on the command line shows this help message

       -q suppress NCL status messages while reading files

       -l<path> reads a file and treats each line of the file as a path to NEXUS file

       -a output AltNexus (no translation table in trees)

       -x do NOT validate internal labels in trees as taxa labels

       -X do NOT treat numbers in trees as taxon numbers, treat them as arbitrary

              labels (should not be used with NEXUS files).

       -s<non-negative integer> controls the NEXUS strictness level.

              the  default  level  is  equivalent  to  -s2 invoking the program with -s3 or a higher number will
              convert some warnings into fatal errors.  Running  with  -s1  will  cause  the  parser  to  accept
              dangerous  constructs,  and  running  with  -s0 will cause the parser make every attempt to finish
              parsing the file (warning about very serious errors).

              Note that when -s0 strictness level is used, and the parser fails to finish, it will often be  the
              result of an earlier error than the error that is reported in the last message.

       -f<format> specifies the input file format expected:

       -fnexus
              NEXUS (this is also the default)

       -faafasta
              Amino acid data in fasta

       -fdnafasta
              DNA data in fasta

       -frnafasta
              RNA data in fasta

              The complete list of format names that can follow the -f flag is:

              nexus
              dnafasta
              aafasta
              rnafasta
              dnaphylip
              rnaphylip
              aaphylip
              discretephylip
              dnaphylipinterleaved
              rnaphylipinterleaved
              aaphylipinterleaved
              discretephylipinterleaved
              dnarelaxedphylip
              rnarelaxedphylip
              aarelaxedphylip
              discreterelaxedphylip
              dnarelaxedphylipinterleaved
              rnarelaxedphylipinterleaved
              aarelaxedphylipinterleaved
              discreterelaxedphylipinterleaved
              dnaaln
              rnaaln
              aaaln
              phyliptree
              relaxedphyliptree
              nexml
              dnafin
              aafin
              rnafin

AUTHOR

       This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage
       of the program.